A systemic investigation of the substitution and cooperative effects on the P…N π-hole pnicogen bond were performed via theoretical calculations. The structural and energetic properties of the binary complexes between a series of substituted benzonitrile and PO2F have been examined to study the substitution effect. The stability of the binary complexes increases in the order of CN
Structural, electronic, topological, vibrational and molecular docking studies have been performed for both enantiomeric S(-) and R(+) forms of potential antiviral to COVID-19 chloroquine (CQ) combining DFT calculations with SQMFF methodology. Hybrid B3LYP/6-311++G** calculations in gas phase and aqueous solution predict few energy differences between both forms. Solvation energies of S(-) and R(+) form are predicted in -55.07 and 59.91 kJ/mol, respectively. Low solvation energies of both forms are justified by the presence of only four donor and acceptor H bonds groups, as compared with other antiviral agents. MK charges on the Cl1, N2, N3 and N4 atoms and AIM calculations could support the high stability of R(+) form in solution according to the higher reactivity predicted for the S(-) form in this medium. Antiviral to COVID-19 niclosamide shows higher reactivity than both forms of CQ. Complete vibrational assignments of 153 vibration modes for both forms and scaled force constants have been reported here. Reasonable concordances were found between predicted and available 1H-NMR, 13C-NMR and UV-Vis spectra. Additionally, NMR and UV-visible spectra suggest the presence of two forms of CQ in solution. A molecular docking study was performed to identify the potency of inhibition of Chloroquine molecule against COVID-19 virus
A series of interatomic interactions interpretable as halogen bonds involving I…I, I…O, and I…C(π), as well as the noncovalent interactions I…H and O…O were observed in the crystal structures of 1,2-diiodoolefins dimers according to ab initio calculations and the quantum theory of “atoms in molecules” (QTAIM) method. The interplay between each type of halogen bond and other noncovalent interactions was studied systematically in terms of bond length, electrostatic potential and interaction energy, which are calculated via ab initio methods at the B3LYP-D3/6-311++G(d,p) and B3LYP-D3/def2-TZVP levels of theory. Characteristics and nature of the haologen bonds and other noncovalent interactions, including the topological properties of the electron density, the charge transfer and their strengthening or weakening, were analyzed by means of both QTAIM and “natural bond order” (NBO). These computational methods provide additional insight into observed intermolecular interactions and are utilized to explain the differences seen in the crystal structures.
Abstract：Efficient reverse intersystem crossing (RISC) is one of the most effective ways to achieve high exciton utilization of pure organic electroluminescent materials. There are two factors affecting the RISC rate (kRISC): the energy difference between the singlet and triplrt excited states (ΔES-T) and the spin-orbit coupling (SOC) between the excited states. In this article, based on the theoretical calculation method which can accurately and quantitatively describe the excited state of the molecule, the typical D-A molecule TPA-NZP is used as a template to study the change of the ΔES-T and the SOC by adjusting the twisting angle of the donor and acceptor in the molecule. By studying the relationship between the excited state transition properties and the SOC, we find that different transition states have a great influence on the coupling. The two excited states are both LE states, but if the phase of the electron cloud are different, which will cause the SOC between them increased greatly; when the transition is the CT state, the SOC matrix elements between the LE state and the CT state both very small; when the singlet and triplet transitions occur in the same part, but the direction of the transition is changed may lead to a huge increase in the SOC.
By doping two potassium atoms among three C20F20 cages, peanut-shaped single molecular solvated dielectron C20F20@K@C20F20@K@C20F20 as new type of spin molecular switches was theoretically presented. The triplet structure with two single-excess-electrons individually inside left and middle cages is thermodynamically more stable than the singlet one with lone pair of excess electrons inside middle cage. It is found that applying an oriented external electric field (OEEF) of 111 × 10-4 au (0.5705 V/Å) or -120 × 10-4 au (-0.6168 V/Å) in the x-axis direction firstly and then releasing it, the field-free triplet C20F20@K@C20F20@K@C20F20 with two single-excess-electrons can change into singlet one with lone pair of excess electrons through a singlet one with lone pair of excess electrons inside the end cage. Different spin states can bring significantly different dipole moment component values and considerable different intensities of maxumum wavelengths in intense absorption band. Therefore, C20F20@K@C20F20@K@C20F20 is a good candidate for spin molecular switching materials.
Due to it is potential application in the field of high energy density materials, how to stabilize cyclopentazolate anion (cyclo-N5-) has attracted many interests theoretically and experimentally. Therefore, a series of ion salts containing [cyclo-N5]- were synthesized and studied. The instability of [cyclo-N5]- is caused by the five lone pairs of electrons localized on five neighbored N atoms. In this work, we expect if the [cyclo-N5]- can be stabilized by the coordination with acidic ligands, by weakening the multi repulsion from the lone pairs to stabilize the [cyclo-N5]-. The two compounds of [N5(BH3)5]-, and [N5(AgCN)5]- have been designed and compared based on the Lewis acid-base theory. [N5(H2O)5]- is designed to evaluate the effect of hydrogen bond in the stabilization. For all the structures, we study the bonding properties and thermal stabilities based on the analysis of electronic structures and Car-Parrinello molecular dynamics (CPMD) simulations. The results indicate it is a effective method to stabilize [cyclo-N5]- by introducing the Lewis acid. Our insights on [cyclo-N5]- compounds with high thermal stability under ambient conditions will provide a new idea for the research and synthesis of new high energetic [cyclo-N5]- series compounds.
Experimentally (G. Mlostoń et al., J. Fluor. Chem. 190 (2016) 56–60), it has been found that the type of the obtained cycloadduct of the [3+2] cycloaddition (32CA) reaction of thiocarbonyl S-methanides with α,β-unsaturated ketones depends strongly on the location of the trifluoromethyl group. In the case of enones containing the CF3CH=CH moiety, the 32CA reaction occurs chemo- and regioselectively onto the C=C double bond giving trifluoromethylated tetrahydrothiophene derivatives. On the other hand, enones containing the CF3–C=O fragment react as carbonyl heteroethylenes leading to trifluoromethylated 1,3-oxathiolanes also in a chemo- and regioselective manner. Our aim in the present work is to perform a theoretical study of the all chemo-, regio-, and stereo-isomeric reaction paths of these 32CA reactions within the Molecular Electron Density Theory. Activation Gibbs free energies, calculated at the B3LYP/6-311G(d,p) level in tetrahydrofurane at -40°C, show that the ortho/endo reaction path giving the trifluoromethylated tetrahydrothiophene is more favoured, while the meta/endo reaction path leading to trifluoromethylated 1,3-oxathiolanes is more preferred in total agreement with experimental findings. The low activation barriers in combination of the Electron Localization Function topological analysis of the most relevant points along the Intrinsic Reaction Coordinate reveals the pseudomonoradical character of the studied 32CA reactions.
Transition metal porphyrazines are a widely used class of compounds with applications in catalysis, organic solar cells, photodynamic therapy and nonlinear optics. The most prominent members of that family of compounds are metallophtalocyanines that have been subject of numerous spectroscopic and theoretical studies. In this work, the electronic structure and X-ray absorption characteristics of three Cu-porphyrazine derivatives are investigated by means of modern electronic structure theory. More precisely, the experimentally observed N K-edge and Cu L-edge features are presented and reproduced by time-dependent density functional theory, restricted open-shell configuration interaction and a restricted active space approach. Where possible, the calculations are used to interpret the observed spectroscopic features in terms of electronic transitions and furthermore connect spectral differences to chemical variations. Part of the discussion of the computational results concerns the impact of various parameters and approximations that enter the calculations, e.g. the choice of active space.
In order to explore the influence of isotope effect and ligand modification on the quantum yield of OLED, three classes Pt(II) complexes with 2,2’-bipyridine ligand have been investigated by using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The explored Pt(II) complexes, class 1 included Pt(RC≡CBpyC≡CR)(C≡CBpy)2, (R = trimethylsilyl，1a or H, 1b, C≡CBpyC≡C = 5,5-bis(ethynyl)-2,2-bipyridine, C≡CBpy corresponds to bipyridineacetylene) and Pt(Bpy)(C≡CBpy)2 (Bpy = bipyridine, 1c); class 2, Pt(Bpy)(C≡CPy)2 (C≡CPy = pyridineacetylene, 2a) , Pt(Bpy)(C≡CPh)2 (C≡CPh =phenylethynyl, 2b), Pt(dbBpy)(C≡CPh)2(dbBpy = 4,4’-di-tert-butyl-2,2’-bipyridine, 2c); and class 3, Pt(Bpy)(Tda) (Tda = tolan-2,2’-diacetylide, 3a), Pt(dbBpy)(Tda) (3b), Pt(3,3’,4,4’-OH-Bpy)(Tda) (3c). The calculation results reveal that the heavy isotope effect effectively reduces the overall vibration frequency of these complexes, and in turn decreases the non-radiative decay rate κnr, which lead to the promotion of phosphorescent quantum yield ϕem. Theoretical studies also reveal the influence of ligand modification on the phosphorescence quantum yields of OLED, and a new Pt(II) complex 3c was designed based on the theoretical study.
Investigation of cooperative effect exhibited by purely C-H—O hydrogen bonded (H-bonded) networks in linear and cyclic clusters of (1,3-cyclohexanedione)n (n = 2 to 6) has been carried out using density functional theoretical calculations. Linear clusters were found to show anti-cooperative behavior, while the cyclic clusters showed positive cooperativity. H-bond strengths and binding energies per bimolecular interaction were found to decrease with increasing cluster size for the linear clusters whereas their cyclic counterparts showed opposite trends. The extent of cooperativity has been found to show monotonic behavior for both linear and cyclic clusters and was found to reach an asymptotic limit with increasing cluster size. Natural bond orbital (NBO) analysis and atoms in molecule (AIM) calculations were found to corroborate the obtained results.
Ferroptosis is a recently characterized form of regulated necrosis with the iron-dependent accumulation of (phospho)lipid hydroperoxides (LOOH). It has attracted considerable attention for its putative involvement in diverse pathophysiological processes, such as cardiovascular disease and neurodegeneration. Here we describe the discovery of tetrahydroquinoxaline, a novel scaffold of ferroptosis inhibitors based on quantum chemistry methods. Tetrahydroquinoxaline deviates showed very good inhibition of ferroptosis, while being non cytotoxic for human cancer cells. And, the advantage of them is their small molecular weight (MW. = 148 Da) that can be coupled with other drugs to form multi-target drugs to better meet the treatment of complicated diseases.
Li-rich layered Mn-based oxides (LMOs) have attracted much attention due to their potential in various applications as cathode materials with high energy density. However, these cathode materials still suffer from drawbacks such as poor rate capability and voltage decay which makes further investigation vital and rational. Herein, the doping strategy is employed to investigate the effect of TM = Ti, Cu, and Zn on Li2Mn0.5TM0.5O3 for improving electrochemical performances of Li2MnO3. The electrochemical properties such as voltage, electrical conductivity, safety, structural stability, and kinetics and mechanism of Li-ion diffusion are evaluated and compared. All doped cathodes decrease the voltage reduction and improve the electrical conductivity coefficient in comparison with LMO. Ti dopants exhibit the potential to increase the maximum voltage of LMO and structural stability. Doping Zn and Cu elements can delay the oxygen loss which leads to a higher life cycle and safety. Also, the substitution of Zn dopants decreases the energy barrier against Li-ion diffusion and consequently, the lower Li-ion diffusion coefficient is expected. Using Ti, Cu, and Zn with α = 0.5 in Li2Mn0.5TMαO3 may furthermore open a door for the synthesis of lithium-rich materials with enhanced performance.
The ligand-promoted palladium-catalyzed hydroarylation of alkynes with arenes without directing group is able to furnish alkenyl chlorides via a 1,4-chlorine migration or trisubstituted alkenes. This reaction is challenging due to bidentate N, N ligand and electron-neutral arenes have rarely been reported to afford good yields. We carried out density functional theory calculations to better understand the elementary steps of the reaction and unveil the ligand effects and origin of substituent-controlled chemoselectivity of challenging C-H activation. For the n-propyl-substituted substrate, CMD process is the rate-determining step of the catalytic reaction. And the chemoselectivity is controlled by oxidative addition with the C-Cl bond cleavage and protonation process. However, for the reaction with 3,5-dimethylphenyl-substituented substrate, the key step of the whole catalytic cycle is the protonation process. The stronger electrostatic attractions, repulsive force and aryl substituent effects result in reverse chemoselectivity. Bidentate ligand L1 (2-OH-1,10-phenanthroline) reacts with Pd(OAc)2 to form a most stable square-planer species, which is different from the one formed by ligand L2(1,10-phenanthroline). The steric repulsion are found to be mainly responsible for no product with L2 as the ligand, which is different from as proviously reported.
Ab initio calculations on systems involving singlet molecular oxygen (O2 (1g)) are challenging due to signicant multi-reference character arising from the degeneracy of the HOMO and LUMO orbitals in singlet oxygen. Here we investigate the stragegy of bypassing singlet oxygen’s multi-reference character by simply adding the experimen- tally determined singlet/triplet splitting (22.5 kcal/mol) to the triplet ground state of molecular oxygen. This method is tested by calculating rate constants for the reac- tions of singlet molecular oxygen with furan, 2-methylfuran, 2,5-dimethylfuran, pyrrole, 2-methylpyrrole, 2,5-dimethylpyrrole, and cyclopentadiene. The calculated rate con- stants are within a factor of 15 compared to experimentally determined rate constants. The results show that energy renement at the CCSD(T)-F12 level of theory is cru- cial to achieving accurate results. The reasonable agreement with experimental values validates the bypassing approach which can be used for other systems involving the 1,4-cyclo-addition of singlet oxygen. 2
Hybrid density functionals have been regularly applied in state-of-the-art computational models for predicting reduction potentials. Benchmark calculations of the absolute reduction potential of ferricenium/ferrocene couple, the IUPAC-proposed reference in nonaqueous solution, include the B3LYP/6-31G(d)/LanL2TZf protocol. We used this procedure to calculate ionization energies and reduction potentials for a comprehensive set of ferrocene derivatives. The protocol works very well for a number of derivatives. However, a significant discrepancy (> 1 V) between experimental and calculated data was detected for selected cases. Three variables were assessed to detect an origin of the observed failure: density functional, basis set, and solvation model. It comes out that the Hartree-Fock exchange fraction in hybrid-DFT methods is the main source of the error. The accidental errors were observed for other hybrid models like PBE0, BHandHLYP, and M06-2X. Therefore, hybrid DFT methods should be used with caution, or pure functionals (BLYP or M06L) may be used instead.
Hydrogen peroxide (H2O2), as clean oxidant, has long suffered from low efficiency and selectivity for the oxidation of olefins. In the present paper, the redox important ferrate anion (FeO42-) has been anchored into a silanol-decorated polyoxometalates (POM) to form single–site supported Fe-POM catalyst. And possible reaction mechanism for the epoxidation of propylene with hydrogen peroxide (H2O2) catalyzed by the Fe-POM catalyst have been investigated based on density functional theory with M06L functional. The study of molecular geometry, electronic structure, and bonding feature shows that the Fe-POM complex can be viewed as a high-valent Fe-oxo (Fe=O) species. The propylene molecule was activated by the Fe-POM catalyst via an effective electron transfer from propylene to the Fe-POM catalyst to form a cation propylene radical. Due to the high reactivity of radical species, the calculated activation energy barrier is only 4.50 kcal mol-1 for epoxidation of propylene to epoxypropane catalyzed by the Fe-POM catalyst. Subsequently, the calculated free energy profiles show that H2O2 was decomposed into a H2O molecule and a surface O species over the Fe-POM catalyst, and the remaining O atom attaches to the exposed the Fe center, resulting in the replenishing of Fe-POM catalyst via a two-state reaction pathway. The calculated activation energy barrier for this process is 23.42 kcal mol–1, and thus decomposition of H2O2 is the rate-determining step for the whole reaction. The Fe center serves as an electron acceptor, accepting electrons from the binding propylene molecule to form radical species in the first half of the reaction, and acts as the role of electron donor in the rest reaction steps to eliminate the radical feature, reduce the reactivity, and stop the reaction at the stage of the desired epoxypropane product.
Reactivity of thymine peroxy radical in DNA and its fate under hypoxia or oxygen-less conditions are studied at the M06-2X/6-31+G(d,p) level. The spaciously most accessible H2’ can be abstracted by C6-peroxy radical in an intranucleotidyl manner with the estimated barriers of 18.8 ~ 21.1 kcal/mol. The calculations show that C6-peroxy radical has a highly more reactivity towards C(sp3)-H abstraction reactions than its relative C6-yl, which is a counter-intuitive case. The formed hydroperoxide with the C6-OaObH2’ constituent can fast transfer ObH2’ group to C2’ radical in an intranucleotidyl manner with a low barrier (ca. 13.2 kcal/mol) and very strong heat release. The results show that the formed hydroperoxide product is unstable so that it could be quickly transformed into other species and thus is very hard to be experimentally observed. Afterwards, H2’ can be again abstracted by C6-oxyl radical to result in formation of thymine glycol which is the main products. The parallel C5-C6 bond scission reaction leads to formation of the precursor for 5-hydroxy-5-methylhydantion. The two competitive reactions have very low barriers. Based on our present calculations, the new radical reaction paths to formation of the DNA oxidation products are suggested under hypoxia or oxygen-less conditions, which is different from the previously suggested paths under high oxygen concentration surroundings.
There are views prevalent in the noncovalent chemistry literature that i) the O atom in molecules cannot form a chalcogen bond, and ii) if formed, this bond is very weak. We have shown here that these views are not necessarily true since the attractive energy between the oxygen atom of some molecules and several electron-rich anionic bases examined in a series of 34 ion-molecule complexes varied from the weak (ca –2.30 kcal mol-1) to the ultra-strong (–90.10 kcal mol-1). The [MP2 /aug-cc-pVTZ] binding energies for several of these complexes were found to be comparable to or significantly larger than that of the well-known hydrogen bond complex [FH···F]– (~ 40 kcal mol-1). The nature of the intermolecular interactions was examined using the quantum theory of atoms in molecules, second-order natural bond orbital and symmetric adaptive perturbation theory energy decomposition analyses. It was found that many of these interactions comprise mixed bonding character (ionic and covalent), especially manifest in the moderate to strongly bound complexes. All these can be explained by an n (lone-pair bonding orbital) -> σ* (anti-bonding orbital) donor-acceptor charge transfer delocalization. This study, therefore, demonstrates that the covalently bound oxygen atom in molecules can have a significant ability to act as an unusually strong chalcogen bond donor.